Flexible Fitting to Infer Atomistic-Precision Models of Large-Amplitude Conformational Dynamics in Biomolecules from...

Area of Science:

• Biophysics
• Computational Biology
• Microscopy

Background:

• High-speed atomic force microscopy (HS-AFM) provides dynamic, single-molecule visualization of biomolecular processes.
• A key limitation is inferring atomistic details from resolution-limited topographic data.
• Developing computational methods to bridge this resolution gap is crucial for understanding molecular mechanisms.

Purpose of the Study:

• To integrate the NMFF-AFM flexible fitting method into the BioAFMviewer software platform.
• To demonstrate the application of this integrated method for inferring atomistic models from HS-AFM data.
• To establish a streamlined workflow for analyzing HS-AFM imaging data and visualizing molecular dynamics.

Main Methods:

• Software integration of the NMFF-AFM flexible fitting algorithm into BioAFMviewer.
• Development of a direct workflow from raw HS-AFM data to analysis and visualization.
• Application of the method to experimental HS-AFM data from protein domains, complexes, and filaments.

Main Results:

• Successful integration of NMFF-AFM into BioAFMviewer, enabling efficient analysis of HS-AFM data.
• Demonstration of the method's versatility in reproducing large-amplitude conformational motions in various biomolecular systems.
• Reconstruction of an atomistic molecular movie of protein dynamics from HS-AFM imaging sequences.

Conclusions:

• The integrated NMFF-AFM flexible fitting method provides a powerful tool for understanding biomolecular dynamics from HS-AFM data.
• This user-friendly software facilitates broad applications for interpreting resolution-limited AFM measurements.
• The ability to generate atomistic molecular movies advances the study of conformational changes in biological systems.